chr2-216632342-G-A

Variant names:

• chr2-216632342-G-A
• rs9341090
• ENST00000793255.1:n.113+3993C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000793255.1(ENSG00000303260):​n.113+3993C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.248 in 151,850 control chromosomes in the GnomAD database, including 4,949 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.25 (4949 hom., cov: 31)
• Consequence: ENSG00000303260 ENST00000793255.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0690
• Publications: 2 publications found

Genes affected

ENSG00000303260 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.282 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000793255.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000303260	ENST00000793255.1		n.113+3993C>T		intron	N/A
	ENSG00000303260	ENST00000793256.1		n.399+578C>T		intron	N/A
	ENSG00000303260	ENST00000793257.1		n.126+818C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.248 AC: 37578 AN: 151728 Hom.: 4944 Cov.: 31

Gnomad AFR AF: 0.243

Gnomad AMI AF: 0.345

Gnomad AMR AF: 0.218

Gnomad ASJ AF: 0.340

Gnomad EAS AF: 0.0258

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.267

Gnomad MID AF: 0.414

Gnomad NFE AF: 0.260

Gnomad OTH AF: 0.261

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.248 AC: 37601 AN: 151850 Hom.: 4949 Cov.: 31 AF XY: 0.249 AC XY: 18436 AN XY: 74186

African (AFR) AF: 0.243 AC: 10081 AN: 41408

American (AMR) AF: 0.217 AC: 3317 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.340 AC: 1180 AN: 3470

East Asian (EAS) AF: 0.0260 AC: 134 AN: 5152

South Asian (SAS) AF: 0.294 AC: 1414 AN: 4804

European-Finnish (FIN) AF: 0.267 AC: 2806 AN: 10522

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.260 AC: 17693 AN: 67924

Other (OTH) AF: 0.257 AC: 541 AN: 2106

Alfa AF: 0.243 Hom.: 559

Bravo AF: 0.244

Asia WGS AF: 0.153 AC: 534 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.5
DANN	Benign	0.80
PhyloP100		0.069
PromoterAI		-0.00060	Neutral

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs9341090; hg19: chr2-217497065;